De novo assembly of the Atlantic herring (Clupea harengus) genome and comparison to a previously published assembly

The Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world and is an important economical and nutritional resource. The Faroe Islands exported herring worth more than 400 million DKK in 2016, which amounts to 5% of the total value of exported goods that year . The species is a highly migratory pelagic species with a complicated population structure. In order to keep the fisheries sustainable, knowledge of subpopulations, their migrations and mixing is important and would assist in the fight against Illegal, Unreported and Unregulated (IUU) fishing.
In 2016 Barrio et al. published the assembled herring genome. Nevertheless as this is a species of such economical and nutritional importance and to gain further information about population structure and standing variation, we have undertaken a second assembly on a different individual using a different mix of sequencing technologies.
Here, we sequenced the herring genome with both Illumina and Oxford Nanopore Technologies platforms. The herring genome was assembled with three different assemblers. AllPaths-LG yielded the best assembly and was then scaffolded using the MinION long reads.
When compared to the previously published assembly, our assembly was more fragmented (12,219 scaffolds and N50 of 219K, compared to 6,915 scaffolds and N50 of 1,860K). However, a Feature-Response curve (FRC) indicated that our assembly had less errors. Nevertheless, aligning the two assemblies indicated no macroscopic structural variations, confirming that our new assembly is a good representation of the Atlantic herring genome.
Assembly completeness is evaluated using the programs BUSCO, QUAST and Reapr. In addition, more MinION data for scaffolding is being produced to improve the scaffolding of our assembly.